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He M, Piscelli BA, Cormanich RA, O’Hagan D. Conformational Analysis Explores the Role of Electrostatic Nonclassical CF···HC Hydrogen Bonding Interactions in Selectively Halogenated Cyclohexanes. J Org Chem 2024; 89:4009-4018. [PMID: 38441063 PMCID: PMC10949234 DOI: 10.1021/acs.joc.3c02868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/06/2024]
Abstract
The conformational equilibria of selectively halogenated cyclohexanes are explored both experimentally (VT-NMR) for 1,1,4,-trifluorocyclohexane 7 and by computational analysis (M06-2X/aug-cc-pVTZ level), with the latter approach extending to a wider range of more highly fluorinated cyclohexanes. Perhaps unexpectedly, 7ax is preferred over the 7eq conformation by ΔG = 1.06 kcal mol-1, contradicting the accepted norm for substituents on cyclohexanes. The axial preference is stronger again in 1,1,3,3,4,5,5,-heptafluorocyclohexane 9 (ΔG = 2.73 kcal mol-1) as the CF2 groups further polarize the isolated CH2 hydrogens. Theoretical decomposition of electrostatic and hyperconjugative effects by natural bond orbital analysis indicated that nonclassical hydrogen bonding (NCHB) between the C-4 fluorine and the diaxial hydrogens at C-2 and C-6 in cyclohexane 7 and 9 largely accounts for the observed bias. The study extended to changing fluorine (F) for chlorine (Cl) and bromine (Br) at the pseudoanomeric position in the cyclohexanes. Although these halogens do not become involved in NCHBs, they polarize the geminal -CHX- hydrogen at the pseudoanomeric position to a greater extent than fluorine, and consequent electrostatic interactions influence conformer stabilities.
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Affiliation(s)
- Mengfan He
- School
of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - Bruno A. Piscelli
- Instituto
de Química, Universidade Estadual
de Campinas (UNICAMP), Monteiro Lobato Street, Campinas, Sao Paulo 13083-862, Brazil
| | - Rodrigo A. Cormanich
- Instituto
de Química, Universidade Estadual
de Campinas (UNICAMP), Monteiro Lobato Street, Campinas, Sao Paulo 13083-862, Brazil
| | - David O’Hagan
- School
of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
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Mondal R, Agbaria M, Nairoukh Z. Fluorinated Rings: Conformation and Application. Chemistry 2021; 27:7193-7213. [PMID: 33512034 DOI: 10.1002/chem.202005425] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 12/16/2022]
Abstract
The introduction of fluorine atoms into molecules and materials across many fields of academic and industrial research is now commonplace, owing to their unique properties. A particularly interesting feature is the impact of fluorine substitution on the relative orientation of a C-F bond when incorporated into organic molecules. In this Review, we will be discussing the conformational behavior of fluorinated aliphatic carbo- and heterocyclic systems. The conformational preference of each system is associated with various interactions introduced by fluorine substitution such as charge-dipole, dipole-dipole, and hyperconjugative interactions. The contribution of each interaction on the stabilization of the fluorinated alicyclic system, which manifests itself in low conformations, will be discussed in detail. The novelty of this feature will be demonstrated by presenting the most recent applications.
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Affiliation(s)
- Rajarshi Mondal
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Mohamed Agbaria
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Zackaria Nairoukh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
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Wu X, Zhou X, Hemberger P, Bodi A. A guinea pig for conformer selectivity and mechanistic insights into dissociative ionization by photoelectron photoion coincidence: fluorocyclohexane. Phys Chem Chem Phys 2020; 22:2351-2360. [PMID: 31934711 DOI: 10.1039/c9cp05617c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We studied fluorocyclohexane (C6H11F, FC6) by double imaging photoelectron photoion coincidence spectroscopy in the 9.90-13.90 eV photon energy range. The photoelectron spectrum can identify species isomer and, in this case, even conformer selectively. Ab initio results indicated that the axial conformer has two, close-lying cation electronic states. With the help of Franck-Condon simulations of the vibrational fine structure, we determined the origin of three transitions, (i) axial FC6 → axial FC6+ of C1 symmetry (X[combining tilde]+, A'' in CS), (ii) equatorial FC6 → equatorial FC6+ of C1 symmetry (X[combining tilde]+, A'' in CS), and (iii) axial FC6 → A' axial FC6+ of CS symmetry (Ã+) as 10.12 ± 0.01, 10.15 ± 0.01 and 10.15 ± 0.02 eV, respectively. At slightly higher energies, the FC6 cation starts fragmenting by HF loss (E0 = 10.60 eV), followed by sequential CH3 (E0 = 10.71 eV) or C2H4 (E0 = 11.06 eV) loss. Surprisingly, the methyl-loss step has an effective barrier of only 0.11 eV, and yet it is a slow process at threshold. Based on the statistical model, this is explained by isomerization and stabilization of the C6H10+ intermediate. The highest energy channel observed, vinyl fluoride (C2H3F) loss yielding C4H8+ appears in the breakdown diagram at 12 eV, which agrees with the computed threshold to cyclobutane cation formation. However, the model predicted a ca. 1 eV competitive shift for this parallel channel, i.e., an E0 = 11.23 eV. This led us to explore the potential energy surface to find a lower-lying fragmentation channel including H-transfer steps. Rate constant measurements and statistical modeling thus yield fundamental insights into the reaction mechanism beyond what is immediately seen in the mass spectra.
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Affiliation(s)
- Xiangkun Wu
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland. and Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China.
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China.
| | - Patrick Hemberger
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland.
| | - Andras Bodi
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland.
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Bis(dicyclohexylselenophosphinyl)selenide, [Cy2P(Se)]2Se: Synthesis, molecular structure and application for self-assembly of a tetrahedral Cu(I) cluster. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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5
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Synthesis of 3-fluoro-3-methyl-3-silatetrahydropyran and its conformational preferences in gas and solution by GED, NMR and theoretical calculations. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.02.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Juanes M, Vogt N, Demaison J, León I, Lesarri A, Rudolph HD. Axial–equatorial isomerism and semiexperimental equilibrium structures of fluorocyclohexane. Phys Chem Chem Phys 2017; 19:29162-29169. [DOI: 10.1039/c7cp06135h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accuracy vs. computational effort: the mixed estimation method provides very accurate semiexperimental equilibrium structures, as illustrated by the subtle differences between axial/equatorial fluorocyclohexane.
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Affiliation(s)
- Marcos Juanes
- Departamento de Química Física y Química Inorgánica
- Facultad de Ciencias
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - Natalja Vogt
- Section of Chemical Information Systems
- University of Ulm
- 89081 Ulm
- Germany
- Department of Chemistry
| | - Jean Demaison
- Section of Chemical Information Systems
- University of Ulm
- 89081 Ulm
- Germany
| | - Iker León
- Departamento de Química Física y Química Inorgánica
- Facultad de Ciencias
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica
- Facultad de Ciencias
- Universidad de Valladolid
- 47011 Valladolid
- Spain
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7
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Conformational stability, infrared and Raman spectra, vibrational assignments, and theoretical calculations of cyclohexylamine. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Zhou SX, Ward RM, Tubergen MJ, Gurusinghe RM, Durig JR. Microwave, infrared, and Raman spectra, r0 structural parameters, conformational stability and ab initio calculations of cyclohexylisocyanate. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2012.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Luo Q, Randall KR, Schaefer HF. Easy chairs: the conformational preferences of polyfluorocyclohexanes. RSC Adv 2013. [DOI: 10.1039/c3ra40538a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Marianski M, Asensio A, Dannenberg JJ. Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives. J Chem Phys 2012; 137:044109. [PMID: 22852599 DOI: 10.1063/1.4737517] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran φ and ψ and C = O...N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95∗∗ to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).
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Affiliation(s)
- Mateusz Marianski
- Department of Chemistry, City University of New York - Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, USA
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Infrared and Raman spectra, conformations, ab initio calculations and spectral assignments of 1-fluoro-1-silacyclohexane. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.02.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Durig JR, Ward RM, Conrad AR, Tubergen MJ, Nelson KG, Gounev TK. Microwave, infrared, and Raman spectra, r0 structural parameters, conformational stability, and vibrational assignment of ethynylcyclohexane. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.03.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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